[English] 日本語
Yorodumi- PDB-7c7q: Cryo-EM structure of the baclofen/BHFF-bound human GABA(B) recept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c7q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the baclofen/BHFF-bound human GABA(B) receptor in active state | |||||||||
Components |
| |||||||||
Keywords | MEMBRANE PROTEIN / GABAB / Cryo-EM / GPCR / active / PAM | |||||||||
Function / homology | Function and homology information negative regulation of gamma-aminobutyric acid secretion / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion ...negative regulation of gamma-aminobutyric acid secretion / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / extracellular matrix protein binding / GABA receptor complex / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic / positive regulation of glutamate secretion / gamma-aminobutyric acid signaling pathway / negative regulation of synaptic transmission / axolemma / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / mitochondrial membrane / response to nicotine / Schaffer collateral - CA1 synapse / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / osteoblast differentiation / transmembrane signaling receptor activity / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Mao, C. / Shen, C. / Li, C. / Shen, D. / Xu, C. / Zhang, S. / Zhou, R. / Shen, Q. / Chen, L. / Jiang, Z. ...Mao, C. / Shen, C. / Li, C. / Shen, D. / Xu, C. / Zhang, S. / Zhou, R. / Shen, Q. / Chen, L. / Jiang, Z. / Liu, J. / Zhang, Y. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Cell Res / Year: 2020 Title: Cryo-EM structures of inactive and active GABA receptor. Authors: Chunyou Mao / Cangsong Shen / Chuntao Li / Dan-Dan Shen / Chanjuan Xu / Shenglan Zhang / Rui Zhou / Qingya Shen / Li-Nan Chen / Zhinong Jiang / Jianfeng Liu / Yan Zhang / Abstract: Metabotropic GABA G protein-coupled receptor functions as a mandatory heterodimer of GB1 and GB2 subunits and mediates inhibitory neurotransmission in the central nervous system. Each subunit is ...Metabotropic GABA G protein-coupled receptor functions as a mandatory heterodimer of GB1 and GB2 subunits and mediates inhibitory neurotransmission in the central nervous system. Each subunit is composed of the extracellular Venus flytrap (VFT) domain and transmembrane (TM) domain. Here we present cryo-EM structures of full-length human heterodimeric GABA receptor in the antagonist-bound inactive state and in the active state complexed with an agonist and a positive allosteric modulator in the presence of G protein at a resolution range of 2.8-3.0 Å. Our structures reveal that agonist binding stabilizes the closure of GB1 VFT, which in turn triggers a rearrangement of TM interfaces between the two subunits from TM3-TM5/TM3-TM5 in the inactive state to TM6/TM6 in the active state and finally induces the opening of intracellular loop 3 and synergistic shifting of TM3, 4 and 5 helices in GB2 TM domain to accommodate the α5-helix of G. We also observed that the positive allosteric modulator anchors at the dimeric interface of TM domains. These results provide a structural framework for understanding class C GPCR activation and a rational template for allosteric modulator design targeting the dimeric interface of GABA receptor. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7c7q.cif.gz | 254 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7c7q.ent.gz | 201.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c7q_validation.pdf.gz | 806 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7c7q_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 7c7q_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 7c7q_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/7c7q ftp://data.pdbj.org/pub/pdb/validation_reports/c7/7c7q | HTTPS FTP |
-Related structure data
Related structure data | 30300MC 7c7sC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 99082.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR1, GPRC3A / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q9UBS5 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 86812.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR2, GPR51, GPRC3B / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: O75899 | ||||||
#3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-FN0 / ( | #5: Chemical | ChemComp-2C0 / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The baclofen/BHFF-bound GABAB heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293F | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Calibrated magnification: 49310 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4624 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3075533 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237606 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7C7S | ||||||||||||||||||||||||||||
Refine LS restraints |
|